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Abstract Many Pacific salmon populations are returning from sea at younger ages and smaller sizes. Hatchery culture, management practices, and environmental factors influence juvenile release size and emigration timing, which in turn affect important demographic characteristics in returning adults. We analyzed data from approximately 345,000 tagged spring Chinook Salmon juveniles exiting Cle Elum Supplementation and Research Facility (Yakima River, Washington, USA) acclimation sites over thirteen brood years (2002–2014), evaluating smolt size, emigration timing, river flow, juvenile survival, and age-at-return. We observed a relationship between size and volitional exit timing of smolts from acclimation sites, with larger fish tending to emigrate earlier than smaller fish. Early emigration was also coincident with lower river flows near acclimation sites. Later emigration timing was correlated with an increase in apparent survival of juveniles to Bonneville Dam (500–530 km downstream of acclimation sites), but also with a lower rate of survival to return from sea. In general, for juveniles successfully emigrating downstream of Bonneville Dam, age-at-return increased with decreasing juvenile fish size and later emigration timing. Our results support a growing body of evidence that hatchery practices may result in larger smolts that tend to return at younger ages. Given the biological and economic consequences of younger age-at-maturation, methods to reverse this trend should be further explored and implemented.

Abstract The Cle Elum Supplementation and Research Facility in the Yakima River basin, Washington, is an integrated spring Chinook Salmon Oncorhynchus tshawytscha hatchery program designed to test whether artificial propagation can increase natural production and harvest opportunities while keeping ecological and genetic impacts within acceptable limits. Only natural-origin (naturally spawned) fish are used for hatchery broodstock. Spawning, incubation, and early rearing occur at a central facility; presmolts are transferred for final rearing, acclimation, and volitional release at sites adjacent to natural spawning areas, where returning adults can spawn with natural-origin fish. The first wild broodstock were collected in 1997, and age-4 adults have returned to the Yakima River since 2001. An unsupplemented population in the adjacent Naches River watershed provides a reference for evaluating environmental influences. The program has been comprehensively monitored from its inception. A synthesis of findings, many already published, is as follows: supplementation increased the harvest, redd counts, and spatial distribution of spawners; natural-origin returns were maintained; straying to nontarget systems was negligible; natural-origin females had slightly higher breeding success (production of surviving fry) in an artificial spawning channel, while the behavior and breeding success of natural- and hatchery-origin males were similar; hatchery-origin fish showed differences in morphometric and life history traits; high rates of hatchery age-2 (minijack) production were reported, but the observed proportions of out-migrating juvenile and adult (ages 4 and 5) returning males were comparable for hatchery- and natural-origin fish; hatchery smolts did not affect the levels of pathogens in natural smolts; and the ecological interactions attributed to the program were within adopted guidelines. Continued study is required to assess the long-term impacts on natural production and productivity.

Abstract Precocious maturation of artificially propagated male Chinook salmon Oncorhynchus tshawytscha has the potential to alter abundance and distribution of males in freshwater and thereby influence ecological and genetic interactions with other fish in the natural environment. Between 1999 and 2007, the Cle Elum Supplementation and Research Facility has produced and released into the upper Yakima River basin of Washington an annual average of 124,573 males that mature precociously. We investigated the abundance and distribution of precociously mature male spring Chinook salmon of hatchery and natural (wild) origin during the spawning season (4–7 months after hatchery release) in the Yakima River. We counted the number of precocious males on the spawning grounds while snorkeling during the peak of spawning and electrofished to determine abundance and distribution of precocious males away from redds. We also collected Chinook salmon to determine percent precocity and size and age distributions. The number of precocious hatchery males on redds was less than 0.05% of the total number of fish released, and they were significantly less abundant on redds than precocious wild males. Between 1999 and 2007, the mean annual abundance of precocious age-1 hatchery males observed on the spawning grounds was 22 fish (range, 0–78). Precocious hatchery and wild males were both found throughout the spawning range during the spawning season, but significant differences in distribution between origins were detected. Precocious hatchery males were proportionately more abundant in the most downstream sampling reach and less abundant in a tributary with no hatchery facilities. In addition, most precocious hatchery males were found downstream of spawning areas during the spawning season. It appears that many precocious hatchery males migrate downstream from release and fail to migrate back to the spawning grounds, or they die within the Yakima River before spawning. Thus, precocious male Chinook salmon resulting from hatchery production in the Yakima River do not contribute favorably to harvest and may pose ecological risks to other taxa, but most of these fish have a low probability of contributing genes to future generations.

Abstract We compared the backpack electrofishing capture efficiencies and Petersen-type mark–recapture abundance estimates of resident rainbow trout Oncorhynchus mykiss that had recovered for 24 h versus 3 h after electrofishing, handling, marking, and release in thirteen 100-m sites in four Yakima River basin tributary streams in central Washington State. Our results indicate that the catchability of rainbow trout was not significantly different between the two recovery periods (P = 0.27). Similarly, Petersen-type mark–recapture abundance estimates did not differ between the two recovery periods (P = 0.20). Despite vigilant effort at installing and maintaining block nets during the 24-h period, we detected fish movement out of 75% of our sites. In addition, our block nets collapsed or were destroyed by small animals in 36% of sites used for a 24-h recovery period; therefore, valid estimates could not be calculated. In contrast, no movement or net failure was detected during the 3-h recovery period. Some of the advantages of a 3-h recovery period between mark–recapture backpack electrofishing events include (1) increased probability of generating a population estimate because of a low threat of block-net failure; (2) lower probability of violating the movement assumption associated with the Petersen-type mark–recapture estimator; and (3) completion of field sampling within a single site visit on a single day. We believe that these advantages should be considered when designing sampling protocols for enumerating stream fish populations.

This report is intended to satisfy two concurrent needs: (1) provide a contract deliverable from the Washington Department of Fish and Wildlife (WDFW) to the Bonneville Power Administration (BPA), with emphasis on identification of salient results of value to ongoing Yakima/Klickitat Fisheries Project (YKFP) planning, and (2) summarize results of research that have broader scientific relevance. This is the thirteenth of a series of progress reports that address species interactions research and supplementation monitoring of fishes in response to supplementation of salmon and steelhead in the upper Yakima River basin (Hindman et al. 1991; McMichael et al. 1992; Pearsons et al. 1993; Pearsons et al. 1994; Pearsons et al. 1996; Pearsons et al. 1998, Pearsons et al. 1999, Pearsons et al. 2001a, Pearsons et al. 2001b, Pearsons et al. 2002, Pearsons et al. 2003, Pearsons et al. 2004). Journal articles and book chapters have also been published from our work (McMichael 1993; Martin et al. 1995; McMichael et al. 1997; McMichael and Pearsons 1998; McMichael et al. 1998; Pearsons and Fritts 1999; McMichael et al. 1999; McMichael et al. 1999; Pearsons and Hopley 1999; Ham and Pearsons 2000; Ham and Pearsons 2001; Amaral et al. 2001; McMichael and Pearsons 2001; Pearsons 2002, Fritts and Pearsons 2004, Pearsons et al. in press, Major et al. in press). This progress report summarizes data collected between January 1, 2004 and December 31, 2004. These data were compared to findings from previous years to identify general trends and make preliminary comparisons. Interactions between fish produced as part of the YKFP, termed target species or stocks, and other species or stocks (non-target taxa) may alter the population status of non-target species or stocks. This may occur through a variety of mechanisms, such as competition, predation, and interbreeding (Pearsons et al. 1994; Busack et al. 1997; Pearsons and Hopley 1999). Furthermore, the success of a supplementation program may be limited by strong ecological interactions such as predation or competition (Busack et al. 1997). Our work has adapted to new information needs as the YKFP has evolved. Initially, our work focused on interactions between anadromous steelhead and resident rainbow trout (for explanation see Pearsons et al. 1993), then interactions between spring chinook salmon and rainbow trout, and recently interactions between spring chinook salmon and highly valued non-target taxa (NTT; e.g., bull trout); and interactions between strong interactor taxa (e.g., those that may strongly influence the abundance of spring chinook salmon; e.g., smallmouth bass) and spring chinook salmon. The change in emphasis to spring chinook salmon has largely been influenced by the shift in the target species planned for supplementation (Bonneville Power Administration et al. 1996; Fast and Craig 1997). Originally, steelhead and spring chinook salmon were proposed to be supplemented simultaneously (Clune and Dauble 1991). However, due in part to the uncertainties associated with interactions between steelhead and rainbow trout, spring chinook and coho salmon were supplemented before steelhead. This redirection in the species to be supplemented has prompted us to prioritize interactions between spring chinook and rainbow trout, while beginning to investigate other ecological interactions of concern. Prefacility monitoring of variables such as rainbow trout density, distribution, and size structure was continued and monitoring of other NTT was initiated in 1997. This report is organized into five chapters that represent major topics associated with monitoring stewardship, utilization, and strong interactor taxa. Chapter 1 reports the results of non-target taxa monitoring after the sixth release of hatchery salmon smolts in the upper Yakima River Basin. Chapter 2 reports on the impacts of supplementation and reintroduction of salmon to trout. Chapter 2 was submitted as a manuscript to the North American Journal of Fisheries Management. Chapter 3 is an essay that describes the problems associated with popular population estimators. This essay was submitted to Fisheries magazine. Chapter 4 describes an evaluation of recovery times on mark-recapture and multiple removal population estimates. Chapter 4 was submitted to the North American Journal of Fisheries Management as a manuscript. Chapter 5, which was submitted as a manuscript to Transactions of the American Fisheries Society, describes the role of predator and prey size in evaluating predation risk by smallmouth bass in the Yakima River. The chapters in this report are in various stages of development and should be considered preliminary unless they have been published in a peer-reviewed journal. Additional field-work and/or analysis is in progress for topics covered in this report.

This report is intended to satisfy two concurrent needs: (1) provide a contract deliverable from the Washington Department of Fish and Wildlife (WDFW) to the Bonneville Power Administration (BPA), with emphasis on identification of salient results of value to ongoing Yakima/Klickitat Fisheries Project (YKFP) planning, and (2) summarize results of research that have broader scientific relevance. This is the twelfth of a series of progress reports that address species interactions research and supplementation monitoring of fishes in response to supplementation of salmon and steelhead in the upper Yakima River basin (Hindman et al. 1991; McMichael et al. 1992; Pearsons et al. 1993; Pearsons et al. 1994; Pearsons et al. 1996; Pearsons et al. 1998, Pearsons et al. 1999, Pearsons et al. 2001a, Pearsons et al. 2001b, Pearsons et al. 2002, Pearsons et al. 2003). Journal articles and book chapters have also been published from our work (McMichael 1993; Martin et al. 1995; McMichael et al. 1997; McMichael and Pearsons 1998; McMichael et al. 1998; Pearsons and Fritts 1999; McMichael et al. 1999; McMichael et al. 1999; Pearsons and Hopley 1999; Ham and Pearsons 2000; Ham and Pearsons 2001; Amaral et al. 2001; McMichael and Pearsons 2001; Pearsons 2002, Fritts and Pearsons 2004, Pearsons et al. in press, Major et al. in press). This progress report summarizes data collected between January 1, 2003 and December 31, 2003. These data were compared to findings from previous years to identify general trends and make preliminary comparisons. Interactions between fish produced as part of the YKFP, termed target species or stocks, and other species or stocks (non-target taxa) may alter the population status of non-target species or stocks. This may occur through a variety of mechanisms, such as competition, predation, and interbreeding (Pearsons et al. 1994; Busack et al. 1997; Pearsons and Hopley 1999). Furthermore, the success of a supplementation program may be limited by strong ecological interactions such as predation or competition (Busack et al. 1997). Our work has adapted to new information needs as the YKFP has evolved. Initially, our work focused on interactions between anadromous steelhead and resident rainbow trout (for explanation see Pearsons et al. 1993), then interactions between spring chinook salmon and rainbow trout, and recently interactions between spring chinook salmon and highly valued non-target taxa (NTT; e.g., bull trout); and interactions between strong interactor taxa (e.g., those that may strongly influence the abundance of spring chinook salmon; e.g., smallmouth bass) and spring chinook salmon. The change in emphasis to spring chinook salmon has largely been influenced by the shift in the target species planned for supplementation (Bonneville Power Administration et al. 1996; Fast and Craig 1997). Originally, steelhead and spring chinook salmon were proposed to be supplemented simultaneously (Clune and Dauble 1991). However, due in part to the uncertainties associated with interactions between steelhead and rainbow trout, spring chinook and coho salmon were supplemented before steelhead. This redirection in the species to be supplemented has prompted us to prioritize interactions between spring chinook and rainbow trout, while beginning to investigate other ecological interactions of concern. Prefacility monitoring of variables such as rainbow trout density, distribution, and size structure was continued and monitoring of other NTT was initiated in 1997. This report is organized into three chapters that represent major topics associated with monitoring stewardship, utilization, and strong interactor taxa. Chapter 1 reports the results of non-target taxa monitoring after the fifth release of hatchery salmon smolts in the upper Yakima River basin. Chapter 2 describes our tributary sampling methodology for monitoring the status of tributary NTT. Chapter 3 describes predation on juvenile salmonids by smallmouth bass and channel catfish in the lower Yakima River. The chapters in this report are in various stages of development and should be considered preliminary unless they have been published in a peer-reviewed journal. Additional field-work and/or analysis is in progress for topics covered in this report. Throughout this report, a premium was placed on presenting data in tables so that other interested parties could have access to the data. Readers are cautioned that any preliminary conclusions are subject to future revision as more data and analytical results become available.